It's a known glitch. Sometimes it happens to me a bunch of times in one day, and some days I never see it happen. Hopefully it will be addressed in an incremental update, or as part of a larger update in the further flung future.

Not from what i've seen. Last time I played a very large battle, with a ship using 4 launchers, 3 of those missiles fail to launch continuously until at least half the ships have been destroyed - no launch sound effect even, just a long delay when the first three should have fired, then the fourth comes out. It's difficult to tell actually whether the missiles are moving and invisible, or they simply disappear. I lose the ammo as well